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There are infrastructure modules (i.e. vcscore) that can provide very generic services (here filesystem). Such services are typically used by many, many, many, ... clients. It's unlikely that all clients release their references to module service objects while disabling the service modules. Original service module zombies remain and can clash with newly enabled services. I think that IDE restart makes sense here (private implementation must exist it's used by IDE updater....). Should be addressed in 5.0 timeframe.
Another (probably better) alternative is to add a "restartOnDisable" attribute into module manifest. This attribute would be handled by module manager. This approach is similar to existing "needsRestart" attribute.
Sorry, won't be addressed in 5.0 timeframe. We're several weeks after the feature freeze.
Regardless of what priority you assign to this issue, it won't be implemented for 5.0. Has this feature been consulted with HIE?
*** Issue 64390 has been marked as a duplicate of this issue. ***
Duplicate. Its already fixed since 6.8. *** This bug has been marked as a duplicate of bug 168257 ***